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LOC132090687 Neanderthal introgressed variant-containing enhancer experimental_56231 [ Homo sapiens (human) ]

Gene ID: 132090687, updated on 12-Sep-2024

Summary

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Gene symbol
LOC132090687
Gene description
Neanderthal introgressed variant-containing enhancer experimental_56231
Gene type
biological region
Feature type(s)
regulatory: enhancer, transcriptional_cis_regulatory_region
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region contains a Neanderthal adaptively introgressed expression-modulating variant (emVar), and was validated as a functional enhancer by massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells, with activity observed for both the introgressed and non-introgressed 2:173533322 or rs16860789 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC132090687 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (172668509..172668678)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (173154984..173155153)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (173533237..173533406)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56026 Neighboring gene integrin subunit alpha 6 Neighboring gene ITGA6 and PDK1 antisense RNA 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56072 Neighboring gene PDK1 and ITGA6 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 994 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:173399678-173400178 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:173413559-173414301 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:173414302-173415043 Neighboring gene Sharpr-MPRA regulatory region 4236 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16763 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12111 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:173456666-173456873 Neighboring gene pyruvate dehydrogenase kinase 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56189 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56221 Neighboring gene Sharpr-MPRA regulatory region 7042 Neighboring gene small nucleolar RNA U13 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56260 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56279 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_56293 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:173577807-173578364 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:173590766-173591266 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:173591267-173591767 Neighboring gene RAPGEF4 antisense RNA 1 Neighboring gene Rap guanine nucleotide exchange factor 4

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells. Jagoda E, et al. Mol Biol Evol, 2022 Jan 7. PMID 34662402, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • emVar-containing allelic enhancer experimental_56231

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_231246.1 

    Range
    101..270
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    172668509..172668678
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    173154984..173155153
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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